Cyp17a1 (cytochrome P450, family 17, subfamily a, polypeptide 1) - Rat Genome Database

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Gene: Cyp17a1 (cytochrome P450, family 17, subfamily a, polypeptide 1) Rattus norvegicus
Analyze
Symbol: Cyp17a1
Name: cytochrome P450, family 17, subfamily a, polypeptide 1
RGD ID: 2456
Description: Enables steroid 17-alpha-monooxygenase activity. Involved in several processes, including animal organ development; response to fungicide; and response to herbicide. Located in cell projection; endoplasmic reticulum; and neuronal cell body. Biomarker of sciatic neuropathy. Human ortholog(s) of this gene implicated in several diseases, including cholelithiasis; congenital adrenal hyperplasia; gallbladder cancer; osteoporosis; and prostate cancer. Orthologous to human CYP17A1 (cytochrome P450 family 17 subfamily A member 1); PARTICIPATES IN 11-beta-hydroxylase deficiency pathway; 17-alpha-hydroxylase deficiency pathway; 21-alpha-hydroxylase deficiency pathway; INTERACTS WITH (+)-schisandrin B; (E)-thiamethoxam; (R)-carnitine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 17-alpha-hydroxyprogesterone aldolase; Cyp17; CYPXVII; cytochrome P450 17A1; Cytochrome P450 subfamily XVII; cytochrome P450, subfamily 17; Cytochrome P450, subfamily XVII; cytochrome P450-C17; cytochrome P450c17; P450-C17; P45017alpha; P450c17; steroid 17-alpha-hydroxylase/17,20 lyase; steroid 17-alpha-monooxygenase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21245,535,462 - 245,543,148 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1245,535,462 - 245,541,573 (-)Ensembl
Rnor_6.01266,422,127 - 266,429,947 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1266,422,132 - 266,428,239 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01273,852,163 - 273,859,866 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41251,965,458 - 251,971,449 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11252,228,608 - 252,234,604 (-)NCBI
Celera1241,321,307 - 241,327,254 (-)NCBICelera
RH 3.4 Map11626.0RGD
Cytogenetic Map1q54NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(E)-thiamethoxam  (EXP)
(R)-carnitine  (EXP)
(R,R)-tramadol  (ISO)
(S)-duloxetine hydrochloride  (ISO)
(S)-nicotine  (EXP,ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP,ISO)
1,1,1-Trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dichloroethane  (ISO)
1,3,4-oxadiazoles  (EXP)
1,3-dinitrobenzene  (ISO)
1-methylnicotinamide  (EXP)
1-naphthylamine  (ISO)
16-Hydroxyprogesterone  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17alpha-hydroxypregnenolone  (ISO)
17alpha-hydroxyprogesterone  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
1H-pyrazole  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,4,7,8-Pentachlorodibenzofuran  (EXP)
2,3,7,8-tetrabromodibenzodioxine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-tribromophenol  (ISO)
2,4-D  (ISO)
2,4-dibromophenol  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dibromophenol  (ISO)
2-bromophenol  (ISO)
2-methoxyethanol  (EXP)
2-trans,6-trans,10-trans-geranylgeranyl diphosphate  (EXP)
2-trans,6-trans-farnesyl diphosphate  (EXP)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP,ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10-heptadecafluoro-1-decanol  (ISO)
3,4-dichloroaniline  (ISO)
3alpha-hydroxy-5beta-pregnan-20-one  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl)benzonitrile  (ISO)
4-nonylphenol  (ISO)
4-octylphenol  (EXP)
4-tert-Octylphenol  (ISO)
5alpha-pregnane-3,20-dione  (ISO)
8-Br-cAMP  (ISO)
abiraterone  (EXP,ISO)
acetaldehyde  (ISO)
acetamide  (EXP)
acetamiprid  (ISO)
Acetyl tributyl citrate  (ISO)
aconitine  (EXP)
aflatoxin B1  (ISO)
albuterol  (ISO)
all-trans-retinoic acid  (EXP,ISO)
allethrin  (EXP)
alpha-naphthoflavone  (ISO)
alternariol  (ISO)
aminoglutethimide  (ISO)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
andrographolide  (ISO)
androst-4-ene-3,17-dione  (ISO)
androsterone  (ISO)
antalarmin  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
apigenin  (ISO)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
astressin  (ISO)
atorvastatin calcium  (EXP)
atrazine  (EXP,ISO)
benomyl  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
berberine  (ISO)
beta-damascenone  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bifenthrin  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (EXP)
bisphenol F  (ISO)
bromobenzene  (EXP)
bucladesine  (EXP)
Butylbenzyl phthalate  (EXP,ISO)
Butylparaben  (EXP)
C60 fullerene  (EXP)
cadmium atom  (EXP)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cetrorelix  (ISO)
chenodeoxycholic acid  (ISO)
chlordecone  (ISO)
chlorohydrocarbon  (EXP)
chloroquine  (EXP)
chlorpyrifos  (ISO)
cholesterol  (ISO)
Chorionic gonadotropin  (EXP,ISO)
chromium(6+)  (EXP)
chrysene  (ISO)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
clotrimazole  (ISO)
colforsin daropate hydrochloride  (ISO)
corticotropin  (ISO)
cyanamide  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP,ISO)
DDE  (EXP)
DDT  (ISO)
decabromodiphenyl ether  (EXP)
dehydroepiandrosterone  (EXP,ISO)
deoxynivalenol  (ISO)
desogestrel  (ISO)
dexamethasone  (EXP,ISO)
Di-n-hexyl phthalate  (EXP)
diarsenic trioxide  (ISO)
dibromoacetic acid  (EXP)
dibutyl phthalate  (EXP,ISO)
diclofenac  (ISO)
Dicyclohexyl phthalate  (EXP)
dienestrol  (EXP)
diethyl phthalate  (EXP,ISO)
diethylstilbestrol  (EXP,ISO)
diheptyl phthalate  (EXP)
diisobutyl phthalate  (EXP,ISO)
diisononyl phthalate  (EXP,ISO)
dipentyl phthalate  (EXP)
disulfiram  (ISO)
drospirenone  (ISO)
endosulfan  (ISO)
enilconazole  (ISO)
enniatin  (ISO)
enzacamene  (EXP)
equol  (ISO)
estrone  (ISO)
etoxazole  (ISO)
farnesyl diphosphate  (EXP)
fenarimol  (ISO)
fenvalerate  (EXP,ISO)
fluconazole  (ISO)
flufenoxuron  (ISO)
flurbiprofen  (EXP,ISO)
flutamide  (EXP,ISO)
folic acid  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
galaxolide  (ISO)
gamma-hexachlorocyclohexane  (ISO)
geldanamycin  (ISO)
genistein  (EXP,ISO)
gentamycin  (EXP)
glafenine  (EXP)
herbicide  (EXP)
hexane  (EXP)
HT-2 toxin  (ISO)
hydrazine  (EXP)
hydroxyflutamide  (ISO)
imidacloprid  (EXP,ISO)
iodoacetic acid  (ISO)
isoflavones  (EXP)
isoliquiritigenin  (ISO)
ketoconazole  (EXP,ISO)
lamotrigine  (ISO)
lead diacetate  (ISO)
leflunomide  (EXP)
letrozole  (EXP)
levetiracetam  (ISO)
levonorgestrel  (ISO)
linuron  (EXP)
lipopolysaccharide  (ISO)
luteolin  (EXP)
metformin  (EXP,ISO)
methotrexate  (ISO)
methoxyacetic acid  (ISO)
methoxychlor  (ISO)
methylmercury chloride  (EXP)
metyrapone  (ISO)
miconazole  (ISO)
Mitotane  (ISO)
mono(2-ethylhexyl) phthalate  (EXP,ISO)
monobenzyl phthalate  (ISO)
Monobutylphthalate  (EXP)
monoethyl phthalate  (ISO)
mycotoxin  (ISO)
N-acetyl-L-cysteine  (EXP)
N-ethyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nickel sulfate  (EXP)
nicotinamide  (EXP)
nicotine  (EXP,ISO)
Nodularin  (EXP)
oxycodone  (EXP)
ozone  (ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
PCB138  (ISO)
pentachlorophenol  (ISO)
perflubron  (ISO)
perfluorododecanoic acid  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phenformin  (EXP)
phenobarbital  (EXP,ISO)
pioglitazone  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
potassium dichromate  (EXP)
pregnenolone  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
prochloraz  (EXP,ISO)
profenofos  (EXP)
progesterone  (EXP,ISO)
prostaglandin E2  (ISO)
pyruvic acid  (ISO)
quercetin  (EXP)
resveratrol  (EXP,ISO)
rotenone  (EXP)
SB 203580  (EXP)
sertraline  (EXP)
simvastatin  (EXP)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sphingosine  (ISO)
sphingosine 1-phosphate  (ISO)
T-2 toxin  (ISO)
tamoxifen  (EXP,ISO)
terbutylazine  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP,ISO)
testosterone enanthate  (EXP,ISO)
Testosterone propionate  (ISO)
testosterone undecanoate  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
tetraphene  (EXP,ISO)
thiamethoxam  (EXP)
titanium dioxide  (ISO)
topiramate  (ISO)
torcetrapib  (ISO)
tramadol  (ISO)
trans-cinnamic acid  (ISO)
triclosan  (EXP)
triphenyl phosphate  (ISO)
triphenylstannane  (EXP)
Triptolide  (ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
tris(2-chloroethyl) phosphate  (ISO)
troglitazone  (EXP,ISO)
uranium atom  (EXP)
valdecoxib  (EXP)
valproic acid  (ISO)
venlafaxine hydrochloride  (ISO)
vinclozolin  (EXP)
zearalenone  (EXP,ISO)
ziram  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Ambrosone CB, etal., Breast Cancer Res. 2003;5(2):R45-51. Epub 2003 Jan 29.
2. Attard G, etal., J Clin Oncol. 2008 Oct 1;26(28):4563-71. Epub 2008 Jul 21.
3. Blystone CR, etal., Toxicol Sci. 2007 Jun;97(2):512-9. Epub 2007 Mar 15.
4. Buczko E, etal., J Steroid Biochem Mol Biol 1995 Mar;52(3):209-18.
5. Carr TL, etal., Arch Toxicol. 2010 Nov 3.
6. Duell EJ, etal., Int J Cancer. 2010 Feb 1;126(3):790-5.
7. Fevold HR, etal., Mol Endocrinol 1989 Jun;3(6):968-75.
8. Fisseha S, etal., Endocrine. 2010 Feb;37(1):187-93. Epub 2009 Dec 15.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. Ghayee HK and Auchus RJ, Rev Endocr Metab Disord. 2007 Dec;8(4):289-300.
11. Givens CR, etal., DNA Cell Biol 1994 Nov;13(11):1087-98.
12. GOA data from the GO Consortium
13. Grasfeder LL, etal., Mol Endocrinol. 2009 Aug;23(8):1171-82. Epub 2009 Apr 23.
14. Grignard E, etal., Int J Toxicol. 2008 Jul-Aug;27(4):323-8.
15. Han DY, etal., Toxicol Ind Health. 2010 Jun;26(5):287-96. Epub 2010 Mar 31.
16. Hou L, etal., Int J Cancer. 2006 Jun 1;118(11):2847-53.
17. Huang HL, etal., J Cell Biochem. 2010 Nov 1;111(4):872-80.
18. Jablonska O, etal., Int J Androl. 2010 Jan 4.
19. Kibaly C, etal., FASEB J. 2008 Jan;22(1):93-104. Epub 2007 Aug 24.
20. Kibaly C, etal., J Neurochem. 2005 Jun;93(5):1220-30.
21. Kimoto T, etal., Endocrinology. 2010 Nov 3.
22. Kumar V, etal., Food Chem Toxicol. 2008 Dec;46(12):3563-70. Epub 2008 Aug 31.
23. Kumar V, etal., Toxicology. 2008 Sep 4;250(2-3):124-31. Epub 2008 Jul 9.
24. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
25. Lahousse SA, etal., Toxicol Sci. 2006 Oct;93(2):369-81. Epub 2006 Jun 29.
26. Li Y, etal., Reprod Biol Endocrinol. 2009 Jul 17;7:73.
27. Mack SO, etal., J Steroid Biochem Mol Biol. 2000 May;73(1-2):19-28.
28. McVey MJ, etal., Food Chem Toxicol. 2008 Jan;46(1):259-69. Epub 2007 Sep 11.
29. McVey MJ, etal., Food Chem Toxicol. 2008 Jan;46(1):270-9. Epub 2007 Aug 14.
30. MGD data from the GO Consortium
31. Miller WL Rev Endocr Metab Disord. 2009 Mar;10(1):3-17.
32. Moustafa GG, etal., Arch Toxicol. 2007 Dec;81(12):875-81. Epub 2007 Jun 14.
33. Munetsuna E, etal., Endocrinology. 2009 Sep;150(9):4260-9. Epub 2009 Jun 4.
34. Namiki M, etal., Biochem Biophys Res Commun 1988 Dec 15;157(2):705-12.
35. NCBI rat LocusLink and RefSeq merged data July 26, 2002
36. Nelson VL, etal., J Clin Endocrinol Metab. 2001 Dec;86(12):5925-33.
37. Nishihara M, etal., Biochem Biophys Res Commun 1988 Jul 15;154(1):151-8.
38. O'Shaughnessy PJ, etal., Reproduction. 2008 Jun;135(6):851-8.
39. OMIM Disease Annotation Pipeline
40. Pelletier G, etal., J Endocrinol. 2001 Nov;171(2):373-83.
41. Pignatelli D, etal., J Endocrinol. 2006 Oct;191(1):301-8.
42. Pipeline to import KEGG annotations from KEGG into RGD
43. Pipeline to import SMPDB annotations from SMPDB into RGD
44. Pogrmic-Majkic K, etal., Toxicol Sci. 2010 Nov;118(1):52-60. Epub 2010 Jul 28.
45. RGD automated data pipeline
46. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
47. RGD automated import pipeline for gene-chemical interactions
48. Ryu JY, etal., J Toxicol Environ Health A. 2008;71(23):1542-9.
49. Shi Z, etal., Toxicol Sci. 2007 Jul;98(1):206-15. Epub 2007 Mar 30.
50. Song L, etal., Steroids. 2010 Mar;75(3):213-8. Epub 2009 Dec 2.
51. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
52. Svechnikov K, etal., J Appl Toxicol. 2009 Nov;29(8):673-80.
53. Svechnikov K, etal., J Endocrinol. 2005 Oct;187(1):117-24.
54. Szoltys M, etal., Acta Histochem. 2010 Nov;112(6):576-82. Epub 2009 Sep 22.
55. Taketoh J, etal., Life Sci. 2007 Mar 13;80(14):1259-67. Epub 2007 Jan 18.
56. Wang H, etal., Hum Reprod. 2005 Oct;20(10):2749-56. Epub 2005 Jun 15.
57. Xiong DH, etal., J Bone Miner Res. 2006 Nov;21(11):1678-95.
58. Yanase T, etal., Endocr Rev. 1991 Feb;12(1):91-108.
59. Zhou W, etal., Mol Cell Endocrinol. 2008 Feb 13;283(1-2):12-8. Epub 2007 Oct 25.
Additional References at PubMed
PMID:1627653   PMID:2554289   PMID:3436956   PMID:7588219   PMID:7588260   PMID:14651853   PMID:14694190   PMID:15169901   PMID:15261307   PMID:15489334   PMID:18556192   PMID:19213837  
PMID:19403566   PMID:21388459   PMID:22170710   PMID:22266943   PMID:22798247   PMID:22800812   PMID:24140098   PMID:24679120   PMID:32438512  


Genomics

Candidate Gene Status
Cyp17a1 is a candidate Gene for QTL Lnnr2
Cyp17a1 is a candidate Gene for QTL Hcar5
Comparative Map Data
Cyp17a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21245,535,462 - 245,543,148 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1245,535,462 - 245,541,573 (-)Ensembl
Rnor_6.01266,422,127 - 266,429,947 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1266,422,132 - 266,428,239 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01273,852,163 - 273,859,866 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41251,965,458 - 251,971,449 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11252,228,608 - 252,234,604 (-)NCBI
Celera1241,321,307 - 241,327,254 (-)NCBICelera
RH 3.4 Map11626.0RGD
Cytogenetic Map1q54NCBI
CYP17A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl10102,830,531 - 102,837,472 (-)EnsemblGRCh38hg38GRCh38
GRCh3810102,830,531 - 102,837,413 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710104,590,288 - 104,597,170 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3610104,580,278 - 104,587,280 (-)NCBINCBI36hg18NCBI36
Build 3410104,580,283 - 104,587,168NCBI
Celera1098,331,010 - 98,337,873 (-)NCBI
Cytogenetic Map10q24.32NCBI
HuRef1098,225,099 - 98,232,065 (-)NCBIHuRef
CHM1_110104,873,550 - 104,880,507 (-)NCBICHM1_1
Cyp17a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391946,655,604 - 46,661,439 (-)NCBIGRCm39mm39
GRCm39 Ensembl1946,655,604 - 46,661,611 (-)Ensembl
GRCm381946,667,165 - 46,673,000 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1946,667,165 - 46,673,172 (-)EnsemblGRCm38mm10GRCm38
MGSCv371946,741,655 - 46,747,490 (-)NCBIGRCm37mm9NCBIm37
MGSCv361946,720,491 - 46,726,285 (-)NCBImm8
Celera1947,437,171 - 47,443,006 (-)NCBICelera
Cytogenetic Map19C3NCBI
cM Map1938.97NCBI
LOC102011010
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554857,645,363 - 7,650,658 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554857,615,132 - 7,652,899 (+)NCBIChiLan1.0ChiLan1.0
CYP17A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110102,891,280 - 102,901,963 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10102,896,376 - 102,901,514 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01099,431,762 - 99,439,619 (-)NCBIMhudiblu_PPA_v0panPan3
CYP17A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12815,292,959 - 15,298,896 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2815,293,106 - 15,298,852 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2815,464,817 - 15,470,751 (-)NCBI
ROS_Cfam_1.02815,766,953 - 15,772,955 (-)NCBI
UMICH_Zoey_3.12815,310,874 - 15,316,795 (-)NCBI
UNSW_CanFamBas_1.02815,350,683 - 15,356,605 (-)NCBI
UU_Cfam_GSD_1.02815,483,290 - 15,489,212 (-)NCBI
LOC101970767
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721331,494,353 - 31,499,609 (+)NCBI
SpeTri2.0NW_0049366003,097,620 - 3,102,713 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYP17A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14113,805,611 - 113,812,041 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114113,805,616 - 113,820,445 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214123,773,108 - 123,787,947 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CYP17A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1995,870,098 - 95,877,345 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl995,866,908 - 95,877,180 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604856,981,761 - 56,989,146 (-)NCBIVero_WHO_p1.0
LOC101726496
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248312,155,851 - 2,166,621 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Mgh24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,542,075 - 245,542,378 (+)MAPPERmRatBN7.2
Rnor_6.01266,428,745 - 266,429,045NCBIRnor6.0
Rnor_5.01273,858,783 - 273,859,083UniSTSRnor5.0
RGSC_v3.41251,972,049 - 251,972,350RGDRGSC3.4
RGSC_v3.41251,972,050 - 251,972,350UniSTSRGSC3.4
RGSC_v3.11252,235,204 - 252,235,505RGD
Celera1241,327,855 - 241,328,155UniSTS
RH 3.4 Map11622.6RGD
RH 3.4 Map11622.6UniSTS
Cytogenetic Map1q55UniSTS
D1Arb47  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,542,203 - 245,542,390 (+)MAPPERmRatBN7.2
Rnor_6.01266,428,873 - 266,429,057NCBIRnor6.0
Rnor_5.01273,858,911 - 273,859,095UniSTSRnor5.0
RGSC_v3.41251,972,177 - 251,972,362RGDRGSC3.4
RGSC_v3.41251,972,178 - 251,972,362UniSTSRGSC3.4
RGSC_v3.11252,235,332 - 252,235,517RGD
Celera1241,327,983 - 241,328,167UniSTS
FHH x ACI Map1129.1099UniSTS
FHH x ACI Map1129.1099RGD
Cytogenetic Map1q55UniSTS
RH94579  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,535,494 - 245,535,594 (+)MAPPERmRatBN7.2
Rnor_6.01266,422,164 - 266,422,263NCBIRnor6.0
Rnor_5.01273,852,200 - 273,852,299UniSTSRnor5.0
RGSC_v3.41251,965,467 - 251,965,566UniSTSRGSC3.4
Celera1241,321,320 - 241,321,419UniSTS
RH 3.4 Map11626.0UniSTS
Cytogenetic Map1q55UniSTS
RH139173  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,535,595 - 245,535,787 (+)MAPPERmRatBN7.2
Rnor_6.01266,422,265 - 266,422,456NCBIRnor6.0
Rnor_5.01273,852,301 - 273,852,492UniSTSRnor5.0
RGSC_v3.41251,965,568 - 251,965,759UniSTSRGSC3.4
Celera1241,321,421 - 241,321,612UniSTS
RH 3.4 Map11626.7UniSTS
Cytogenetic Map1q55UniSTS
PMC85975P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,535,648 - 245,536,352 (+)MAPPERmRatBN7.2
Rnor_6.01266,422,318 - 266,423,021NCBIRnor6.0
Rnor_5.01273,852,354 - 273,853,057UniSTSRnor5.0
RGSC_v3.41251,965,621 - 251,966,324UniSTSRGSC3.4
Celera1241,321,474 - 241,322,177UniSTS
Cytogenetic Map1q55UniSTS
UniSTS:464662  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,537,627 - 245,537,744 (+)MAPPERmRatBN7.2
Rnor_6.01266,424,299 - 266,424,415NCBIRnor6.0
Rnor_5.01273,854,335 - 273,854,451UniSTSRnor5.0
RGSC_v3.41251,967,602 - 251,967,718UniSTSRGSC3.4
Celera1241,323,454 - 241,323,570UniSTS
Cytogenetic Map1q55UniSTS
UniSTS:257093  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21245,539,047 - 245,539,551 (+)MAPPERmRatBN7.2
Rnor_6.01266,425,719 - 266,426,222NCBIRnor6.0
Rnor_5.01273,855,755 - 273,856,258UniSTSRnor5.0
RGSC_v3.41251,969,022 - 251,969,525UniSTSRGSC3.4
Celera1241,324,875 - 241,325,378UniSTS
Cytogenetic Map1q55UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1233948574260522016Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
2316896Gluco57Glucose level QTL 577.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1228985440245907899Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1218753689245907899Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:119
Count of miRNA genes:98
Interacting mature miRNAs:109
Transcripts:ENSRNOT00000027160
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 2
Medium 1 15 15 15 21
Low 2 11 24 22 1 22 2 2 8 10 11 1 2
Below cutoff 24 17 4 11 4 1 3 39 19 3 6 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027160   ⟹   ENSRNOP00000027160
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1245,535,462 - 245,541,573 (-)Ensembl
Rnor_6.0 Ensembl1266,422,132 - 266,428,239 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102611   ⟹   ENSRNOP00000086774
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1245,536,198 - 245,541,573 (-)Ensembl
RefSeq Acc Id: NM_012753   ⟹   NP_036885
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,535,462 - 245,543,148 (-)NCBI
Rnor_6.01266,422,151 - 266,428,144 (-)NCBI
Rnor_5.01273,852,163 - 273,859,866 (-)NCBI
RGSC_v3.41251,965,458 - 251,971,449 (-)RGD
Celera1241,321,307 - 241,327,254 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036885   ⟸   NM_012753
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000027160   ⟸   ENSRNOT00000027160
RefSeq Acc Id: ENSRNOP00000086774   ⟸   ENSRNOT00000102611

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13690971
Promoter ID:EPDNEW_R1495
Type:multiple initiation site
Name:Cyp17a1_1
Description:cytochrome P450, family 17, subfamily a, polypeptide 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01266,428,155 - 266,428,215EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2456 AgrOrtholog
Ensembl Genes ENSRNOG00000020035 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027160 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027160 UniProtKB/TrEMBL
Gene3D-CATH 1.10.630.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7111017 IMAGE-MGC_LOAD
InterPro Cyt_P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_E_grp-I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyt_P450_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25146 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93633 IMAGE-MGC_LOAD
NCBI Gene 25146 ENTREZGENE
Pfam p450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cyp17a1 PhenoGen
PRINTS EP450I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CYTOCHROME_P450 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48264 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JSR8_RAT UniProtKB/TrEMBL
  CP17A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q68FY2 UniProtKB/Swiss-Prot
  Q6LAE5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Cyp17a1  cytochrome P450, family 17, subfamily a, polypeptide 1  Cyp17  cytochrome P450, subfamily 17  Symbol and Name updated 1299863 APPROVED
2002-11-06 Cyp17  cytochrome P450, subfamily 17    Cytochrome P450, subfamily XVII  Name updated 625702 APPROVED
2002-06-10 Cyp17  Cytochrome P450, subfamily XVII      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains two trans-membrane regions anchor the N terminus to the ER membrane 1298834
gene_function catalyzes both delta 4- and delta 5-steroid-17,20-lyase reactions when transfected into COS cells 1298835
gene_homology moderate homology to human, bovine and chicken cyp17 1298835
gene_regulation cAMP inducible via a non-CREB pathway 1298833